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- PDB-7xi4: Crystal Structure of the NPAS4-ARNT heterodimer in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7xi4
TitleCrystal Structure of the NPAS4-ARNT heterodimer in complex with DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • DNA (5'-D(*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')
  • DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')
  • Neuronal PAS domain protein 4
KeywordsTRANSCRIPTION / protein-DNA complex
Function / homology
Function and homology information


Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation ...Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / response to toxic substance / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / cell differentiation / nuclear body / protein dimerization activity / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Neuronal PAS domain protein 4 / Aryl hydrocarbon receptor nuclear translocator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.707 Å
AuthorsSun, X.N. / Jing, L.Q. / Li, F.W. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentZR2021JQ30 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family.
Authors: Sun, X. / Jing, L. / Li, F. / Zhang, M. / Diao, X. / Zhuang, J. / Rastinejad, F. / Wu, D.
History
DepositionApr 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator
B: Neuronal PAS domain protein 4
C: DNA (5'-D(*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)92,4854
Polymers92,4854
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-90 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.243, 105.243, 215.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF-1- ...ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF-1-beta / HIF1-beta


Mass: 43306.199 Da / Num. of mol.: 1 / Fragment: ARNT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Plasmid: pMKH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53762
#2: Protein Neuronal PAS domain protein 4


Mass: 39381.828 Da / Num. of mol.: 1 / Fragment: NPAS4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Npas4 / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A1L327
#3: DNA chain DNA (5'-D(*GP*GP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*TP*GP*AP*T)-3')


Mass: 5034.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*CP*CP*AP*TP*CP*AP*CP*TP*CP*AP*CP*GP*AP*CP*CP*T)-3')


Mass: 4763.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.91 % / Mosaicity: 0.499 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8 / Details: ammonium tartrate dibasic, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: SIEMENS-NICOLET / Detector: PIXEL / Date: Jun 26, 2019 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 4.7→50 Å / Num. obs: 6762 / % possible obs: 99.9 % / Redundancy: 23.3 % / Biso Wilson estimate: 57.49 Å2 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.054 / Rrim(I) all: 0.267 / Χ2: 0.977 / Net I/σ(I): 2.4 / Num. measured all: 157818
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.7-4.7819.71.8243270.6550.411.8730.96799.4
4.78-4.8721.62.2383120.5830.4852.2921.011100
4.87-4.9622.42.0773400.650.4392.1241.001100
4.96-5.0624.42.0423180.8040.4152.0850.965100
5.06-5.1724.71.7113230.8410.3461.7460.994100
5.17-5.2924.61.5213410.8690.3071.5520.98100
5.29-5.4224.91.5433230.9090.3121.5750.988100
5.42-5.5723.81.3743400.860.2841.4040.985100
5.57-5.7423.61.2583220.8940.2611.2860.989100
5.74-5.9222.11.0033290.8650.2171.0281.017100
5.92-6.1321.20.9033370.9180.2010.9261.01298.8
6.13-6.3824.50.8993310.90.1840.9181.052100
6.38-6.6726.40.7013320.9670.1380.7141.04100
6.67-7.0226.20.533410.980.1050.5410.976100
7.02-7.4525.90.3713440.9840.0740.3791.017100
7.45-8.0325.80.2623310.9940.0520.2671.021100
8.03-8.8324.20.1483520.9980.030.1510.998100
8.83-10.122.90.0853490.9990.0180.0870.919100
10.1-12.6919.60.0533660.9990.0120.0540.848100
12.69-5019.40.044040.9990.0090.0410.741100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPK

4zpk


Resolution: 4.707→29.63 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3506 298 5.25 %
Rwork0.3136 5379 -
obs0.3155 5677 84.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 270.74 Å2 / Biso mean: 109.9629 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 4.707→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 634 0 0 5300
Num. residues----620
LS refinement shellResolution: 4.707→4.78 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3555 134 -
Rwork0.3116 2219 -
obs--72 %

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